Debugging basic MCP functionality, added simple MCP file management

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -3407,8 +3407,13 @@ public class CLTParameters {
 	}
 
 	public boolean showJDialog() {
+		return showJDialog(false);
+	}
+
+	// codex 2026-01-27: optional modeless dialog for MCP/GUI co-use
+	public boolean showJDialog(boolean nonBlocking) {
 		//  			GenericDialog gd = new GenericDialog("Set CLT parameters");
-		GenericJTabbedDialogMcp gd = new GenericJTabbedDialogMcp("Set CLT parameters",1090,900); // codex 2026-01-25
+		GenericJTabbedDialogMcp gd = new GenericJTabbedDialogMcp("Set CLT parameters",1090,900, !nonBlocking); // codex 2026-01-25
 		gd.addTab         ("General", "General parameters");
 		gd.addNumericField("Nominal (rectilinear) disparity between side of square cameras (pix)",              this.disparity,  3,7,"pix",
 				"Used when rendering 4 images");
@@ -4926,6 +4931,17 @@ public class CLTParameters {
 
 
 		//  			gd.buildDialog();
+			if (nonBlocking && !gd.mcp_mode) {
+				gd.setOnOk(new Runnable() {
+					@Override
+					public void run() {
+						gd.resetReadPosition();
+						applyCltDialog(gd);
+					}
+				});
+				gd.showDialogNonBlocking();
+				return true;
+			}
 		gd.showDialog();
 		//  			System.out.println("gd.wasCanceled="+gd.wasCanceled());
 		/*
@@ -4933,6 +4949,12 @@ public class CLTParameters {
   			WindowTools.addScrollBars(gd);
   			gd.showDialog();
 		 */
+			return applyCltDialog(gd);
+	}
+
+
+	// codex 2026-01-27: apply dialog values after OK
+	private boolean applyCltDialog(GenericJTabbedDialogMcp gd) {
 		if (gd.wasCanceled()) return false;
 		this.disparity=             gd.getNextNumber();
 		this.transform_size=  (int) gd.getNextNumber();
@@ -5964,7 +5986,6 @@ public class CLTParameters {
 		return true;
 	}
 
-
 	public boolean showTsDialog() {
 		GenericDialog gd = new GenericDialog("Set CLT tiles to surfaces assignment parameters");
 		gd.addCheckbox    ("Do not assign tiles to the surface edges (not having all 8 neighbors)",                     this.tsNoEdge);
@@ -6120,8 +6141,10 @@ public class CLTParameters {
 		this.taEnWeakFgnd=          gd.getNextBoolean();
 		this.taEnFlaps=             gd.getNextBoolean();
 		this.taEnMismatch=          gd.getNextBoolean();
+
 		return true;
 	}
+
 	public boolean modifyZCorr (String title) {
 		if (z_corr_map == null){
 			z_corr_map = new HashMap<String,Double>();

src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java

@@ -1197,7 +1197,14 @@ public class EyesisCorrectionParameters {
 
     	public boolean showCLTBatchDialog(String title,
     			CLTParameters clt_parameters) {
-    		GenericJTabbedDialogMcp gd = new GenericJTabbedDialogMcp(title,1000,1000); // codex 2026-01-25
+    		return showCLTBatchDialog(title, clt_parameters, false);
+    	}
+
+    	// codex 2026-01-27: optional modeless dialog for MCP/GUI co-use
+    	public boolean showCLTBatchDialog(String title,
+    			CLTParameters clt_parameters,
+    			boolean nonBlocking) {
+    		GenericJTabbedDialogMcp gd = new GenericJTabbedDialogMcp(title,1000,1000, !nonBlocking); // codex 2026-01-25
     		updateAuxFromMain();
 
 
@@ -1402,7 +1409,25 @@ public class EyesisCorrectionParameters {
 
     		}
 //    		WindowTools.addScrollBars(gd);
+    		if (nonBlocking && !gd.mcp_mode) {
+    			gd.setOnOk(new Runnable() {
+    				@Override
+    				public void run() {
+    					gd.resetReadPosition();
+    					applyCltBatchDialog(gd, clt_parameters);
+    				}
+    			});
+    			gd.showDialogNonBlocking();
+    			return true;
+    		}
     		gd.showDialog();
+    		return applyCltBatchDialog(gd, clt_parameters);
+
+    	}
+
+    	// codex 2026-01-27: apply dialog values after OK
+    	private boolean applyCltBatchDialog(GenericJTabbedDialogMcp gd,
+    			CLTParameters clt_parameters) {
     		if (gd.wasCanceled()) return false;
 
     		this.tile_processor_gpu =    gd.getNextString(); if (gd.getNextBoolean()) selectGPUSourceDirectory(false, false);
@@ -1767,7 +1792,7 @@ public class EyesisCorrectionParameters {
             	base_path=base_path.resolve(Paths.get(dir_map.get("rootDirectory")));
     			File base_dir = new File(base_path.toString());
     			if (!base_dir.exists()) {
-    				base_dir.mkdirs();
+    				base_dir.mkdirs(); // codex 2026-01-28: mkdirs side-effect (consider guarding)
     			}
             }
             // set sourceDirectory: 
@@ -1783,7 +1808,7 @@ public class EyesisCorrectionParameters {
     		Path source_path = Paths.get(this.sourceDirectory);
 			File source_dir = new File(source_path.toString());
 			if (!source_dir.exists()) {
-				source_dir.mkdirs();
+				source_dir.mkdirs(); // codex 2026-01-28: mkdirs side-effect (consider guarding)
 			}
 			
             useCuasSeedDir = false;
@@ -1796,7 +1821,7 @@ public class EyesisCorrectionParameters {
             			File dir_file = new File(dir_path.toString());
             			if ((i != KEY_INDEX_UAS_LOGS) && (i != KEY_INDEX_SKY_MASK)) { // cuasUasLogs, cuasSkyMask are files, not directories
             				if (!dir_file.exists()) {
-            					dir_file.mkdirs();
+            					dir_file.mkdirs(); // codex 2026-01-28: mkdirs side-effect (consider guarding)
             				}
             			}
             			dir_string =  dir_path.toString();

src/main/java/com/elphel/imagej/common/GenericJTabbedDialog.java

@@ -48,12 +48,20 @@ public class GenericJTabbedDialog implements ActionListener {
 	private int read_tab=0,read_component=0; // current number of tab/component to be read next
 	String result=null;
 	private JDialog jd;
+	// codex 2026-01-27: optional callbacks for modeless dialogs
+	private Runnable onOk;
+	private Runnable onCancel;
 	public GenericJTabbedDialog(String title) {
 		this(title, 600, 800);
 	}
 	public GenericJTabbedDialog(String title, int width, int height) {
+		this(title, width, height, true);
+	}
+
+	// codex 2026-01-27: allow modeless dialog for non-blocking UI
+	public GenericJTabbedDialog(String title, int width, int height, boolean modal) {
 //		final JFrame frame= new JFrame();
-		jd = new JDialog(frame , title, true);
+		jd = new JDialog(frame , title, modal);
 		components.add(new ArrayList<JComponent>());
 		labels.add(new ArrayList<JLabel>());
 		tabs.add (new JPanel(false)); // first (yet nameless tab)
@@ -341,14 +349,48 @@ public class GenericJTabbedDialog implements ActionListener {
             return false;
         }
 
+        // codex 2026-01-27: modeless dialog
+        public void showDialogNonBlocking() {
+        	buildDialog();
+        	jd.setVisible(true);
+        }
+
+        // codex 2026-01-27: reset read cursor before applying values
+        public void resetReadPosition() {
+        	read_tab = 0;
+        	read_component = 0;
+        }
+
+        // codex 2026-01-27: callbacks for modeless dialogs
+        public void setOnOk(Runnable onOk) {
+        	this.onOk = onOk;
+        }
+
+        public void setOnCancel(Runnable onCancel) {
+        	this.onCancel = onCancel;
+        }
+
+        // codex 2026-01-27: allow external close (for MCP/GUI coordination)
+        public void closeDialog() {
+        	if (jd != null) {
+        		jd.dispose();
+        	}
+        }
+
     @Override
 	public void actionPerformed(ActionEvent e) {
 //    	System.out.println(e.getActionCommand());
     	if (e.getActionCommand().equals("Cancel")) {
     		result = e.getActionCommand();
+    		if (onCancel != null) {
+    			onCancel.run();
+    		}
     		jd.dispose();
     	} else if (e.getActionCommand().equals("OK")) {
     		result = e.getActionCommand();
+    		if (onOk != null) {
+    			onOk.run();
+    		}
     		jd.dispose();
     		// Added 07/18/2021 - button names starting with "_" exit from dialog
     	} else if ((e.getActionCommand().length()>0) && (e.getActionCommand().charAt(0) == '_')){

src/main/java/com/elphel/imagej/common/GenericJTabbedDialogMcp.java

@@ -27,11 +27,21 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 		this.dialogTitle = title;
 		this.mcp_mode = defaultMcpMode;
 	}
+	// codex 2026-01-27: allow modeless dialog creation
+	public GenericJTabbedDialogMcp(String title, int width, int height, boolean modal) {
+		super(title, width, height, modal);
+		this.dialogTitle = title;
+		this.mcp_mode = defaultMcpMode;
+	}
 
 	// codex 2026-01-25: global MCP mode default
 	public static void setDefaultMcpMode(boolean enabled) {
 		defaultMcpMode = enabled;
 	}
+	// codex 2026-01-27: expose MCP mode default
+	public static boolean isDefaultMcpMode() {
+		return defaultMcpMode;
+	}
 
 	private void addMcpField(McpDialogField field) {
 		mcpFields.add(field);
@@ -248,6 +258,14 @@ public class GenericJTabbedDialogMcp extends GenericJTabbedDialog{
 		else return super.showDialog();
 	}
 
+	// codex 2026-01-27: modeless dialog for GUI mode
+	public void showDialogNonBlocking() {
+		if (mcp_mode) {
+			buildDialog();
+		}
+		else super.showDialogNonBlocking();
+	}
+
 	@Override
 	public String showDialogAny() {
 		if (mcp_mode) {

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -67,6 +67,7 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Comparator;
 import java.util.EnumSet;
+import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Properties;
@@ -120,6 +121,7 @@ import com.elphel.imagej.gpu.JCuda_ImageJ_Example_Plugin;
 import com.elphel.imagej.ims.DjiSrt;
 import com.elphel.imagej.ims.DjiSrtReader;
 import com.elphel.imagej.mcp.McpServer;
+import com.elphel.imagej.mcp.FileSelectMcp;
 import com.elphel.imagej.ims.EventLogger;
 import com.elphel.imagej.ims.QuatVertLMA;
 import com.elphel.imagej.ims.UasLogReader;
@@ -475,6 +477,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	public static ImageStack convolutionKernelStack2 = null; // select to use for image convolution
 	public static ImagePlus imp_gaussian = null;
 	public static String DEFAULT_DIRECTORY = null;
+	// codex 2026-01-28: remember last MCP-selected paths per dialog title
+	private static final HashMap<String, String> MCP_LAST_PATHS = new HashMap<String, String>();
 	public static boolean ADVANCED_MODE = false; // true; // show all buttons
 	public static boolean DCT_MODE = false; // true; // show all buttons
 	public static boolean MODE_3D = false; // 3D-related commands
@@ -531,6 +535,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		LogTee.install();         // once, early
 		// codex 2026-01-25: start MCP server + enable MCP dialog mode by default
 		GenericJTabbedDialogMcp.setDefaultMcpMode(getMcpMode());
+		// codex 2026-01-27: enable MCP-mode SyncCommand control
+		SYNC_COMMAND.setMcpMode(getMcpMode());
 		McpServer.startIfNeeded(this, getMcpPort());
 		// codex 2026-01-25: optional SLF4J/logback root level override
 		applySlf4jRootLevel();
@@ -1565,6 +1571,23 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		return this.SYNC_COMMAND.buttonLabel;
 	}
 
+	// codex 2026-01-27: MCP interrupt controls
+	public boolean requestSyncStop(boolean confirm, boolean asap) {
+		return this.SYNC_COMMAND.requestStop(confirm, asap);
+	}
+
+	public boolean confirmSyncStop(boolean stop) {
+		return this.SYNC_COMMAND.confirmStop(stop);
+	}
+
+	public boolean isSyncConfirmPending() {
+		return this.SYNC_COMMAND.isConfirmPending();
+	}
+
+	public boolean isSyncConfirmConvenient() {
+		return this.SYNC_COMMAND.isConfirmConvenient();
+	}
+
 	private int getMcpPort() {
 		String value = System.getProperty("elphel.mcp.port");
 		if (value == null || value.isEmpty()) {
@@ -4739,16 +4762,16 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			/* ======================================================================== */
 		} else if (label.equals("Setup CLT Batch parameters")) {
 			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
-			CORRECTION_PARAMETERS.showCLTBatchDialog("CLT Batch parameters", CLT_PARAMETERS);
+			CORRECTION_PARAMETERS.showCLTBatchDialog("CLT Batch parameters", CLT_PARAMETERS, true); // codex 2026-01-27
 			return;
 
 			/* ======================================================================== */
 		} else if (label.equals("Setup CLT parameters")) {
-			CLT_PARAMETERS.showJDialog();
+			CLT_PARAMETERS.showJDialog(true); // codex 2026-01-27
 			return;
 			/* ======================================================================== */
 		} else if (label.equals("Setup CLT")) {
-			CLT_PARAMETERS.showJDialog();
+			CLT_PARAMETERS.showJDialog(true); // codex 2026-01-27
 			return;
 			/* ======================================================================== */
 		} else if (label.equals("Infinity offset")) {
@@ -10139,6 +10162,27 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 
 	public static String[] selectDirectoriesOrFiles(boolean save, boolean directory, String title, String button,
 			FileFilter filter, String[] defaultPaths) {
+		if (GenericJTabbedDialogMcp.isDefaultMcpMode()) {
+			String defaultPath = null;
+			if (defaultPaths != null && defaultPaths.length > 0) {
+				defaultPath = defaultPaths[0];
+			}
+			String key = (title == null || title.isEmpty()) ? "default" : title;
+			String initial = defaultPath;
+			if (initial == null || initial.isEmpty()) {
+				initial = MCP_LAST_PATHS.get(key);
+			}
+			if (initial == null || initial.isEmpty()) {
+				initial = DEFAULT_DIRECTORY;
+			}
+			String[] selected = FileSelectMcp.selectMultiple(directory, title, initial);
+			if (selected == null || selected.length == 0) {
+				return null;
+			}
+			updateDefaultDirectoryFromPath(selected[0], directory);
+			MCP_LAST_PATHS.put(key, selected[0]);
+			return selected;
+		}
 		File dir = null;
 		String defaultPath = null;
 		File[] files = null;
@@ -10211,6 +10255,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 
 	public static String selectDirectoryOrFile(boolean save, boolean directory, String title, String button, FileFilter filter,
 			String defaultPath) {
+		if (GenericJTabbedDialogMcp.isDefaultMcpMode()) {
+			return selectDirectoryOrFileMcp(directory, title, defaultPath);
+		}
 		File dir = null;
 		if ((defaultPath != null) && (!defaultPath.equals(""))) {
 			dir = new File(defaultPath);
@@ -10250,6 +10297,44 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		DEFAULT_DIRECTORY = fc.getCurrentDirectory().getPath();
 		return fc.getSelectedFile().getPath();
 	}
+
+	// codex 2026-01-28: MCP file selection helper (single path)
+	private static String selectDirectoryOrFileMcp(boolean directory, String title, String defaultPath) {
+		String key = (title == null || title.isEmpty()) ? "default" : title;
+		String initial = defaultPath;
+		if (initial == null || initial.isEmpty()) {
+			initial = MCP_LAST_PATHS.get(key);
+		}
+		if (initial == null || initial.isEmpty()) {
+			initial = DEFAULT_DIRECTORY;
+		}
+		String value = FileSelectMcp.selectSingle(directory, title, initial);
+		if (value == null) {
+			return null;
+		}
+		updateDefaultDirectoryFromPath(value, directory);
+		MCP_LAST_PATHS.put(key, value);
+		return value;
+	}
+
+	// codex 2026-01-28: update DEFAULT_DIRECTORY from a selected path
+	private static void updateDefaultDirectoryFromPath(String value, boolean directory) {
+		if (value == null || value.isEmpty()) {
+			return;
+		}
+		File selected = new File(value);
+		if (directory && !selected.isDirectory()) {
+			return;
+		}
+		if (selected.isDirectory()) {
+			DEFAULT_DIRECTORY = selected.getPath();
+		} else {
+			File parent = selected.getParentFile();
+			if (parent != null) {
+				DEFAULT_DIRECTORY = parent.getPath();
+			}
+		}
+	}
 /*
 	class MultipleExtensionsFileFilter extends FileFilter {
 		protected String[] patterns;

src/main/java/com/elphel/imagej/correction/SyncCommand.java

@@ -12,6 +12,49 @@ public class SyncCommand {
 	public AtomicInteger stopRequested = new AtomicInteger(0); // 0 - not requested, 1 - ASAP, 2 - gracefully
 	public String buttonLabel = "";
 	public boolean confirm = true;
+	// codex 2026-01-27: MCP-controlled pause/confirm
+	private boolean mcpMode = false;
+	private boolean confirmPending = false;
+	private Boolean confirmDecision = null;
+	private boolean confirmConvenient = false;
+	private GenericJTabbedDialog confirmDialog = null;
+
+	// codex 2026-01-27: enable MCP mode (non-GUI confirm)
+	public void setMcpMode(boolean enabled) {
+		this.mcpMode = enabled;
+	}
+
+	// codex 2026-01-27: request stop via MCP
+	public boolean requestStop(boolean confirm, boolean asap) {
+		this.confirm = confirm;
+		this.stopRequested.set(asap ? STOP_ASAP : STOP_CONVENIENT);
+		return true;
+	}
+
+	// codex 2026-01-27: confirm/cancel stop via MCP
+	public boolean confirmStop(boolean stop) {
+		synchronized (this) {
+			if (!confirmPending) {
+				return false;
+			}
+			confirmDecision = Boolean.valueOf(stop);
+			confirmPending = false;
+			if (confirmDialog != null) {
+				confirmDialog.closeDialog();
+				confirmDialog = null;
+			}
+			this.notifyAll();
+		}
+		return true;
+	}
+
+	public boolean isConfirmPending() {
+		return confirmPending;
+	}
+
+	public boolean isConfirmConvenient() {
+		return confirmConvenient;
+	}
 	
 	public boolean interruptCommand() {
 		boolean asap = false;
@@ -38,6 +81,54 @@ public class SyncCommand {
 		if (!confirm) {
 			return true;
 		}
+		if (mcpMode) {
+			synchronized (this) {
+				confirmPending = true;
+				confirmConvenient = convenient;
+				confirmDecision = null;
+				stopRequested.set(STOP_NO); // reset pending stop in any case.
+				confirmDialog = new GenericJTabbedDialog(
+						"Stop requested, " + (convenient ? "convenient point" : "ASAP point"), 600, 300, false);
+				confirmDialog.addMessage("OK to stop, Cancel to continue");
+				confirmDialog.setOnOk(new Runnable() {
+					@Override
+					public void run() {
+						synchronized (SyncCommand.this) {
+							confirmDecision = Boolean.TRUE;
+							confirmPending = false;
+							confirmDialog = null;
+							SyncCommand.this.notifyAll();
+						}
+					}
+				});
+				confirmDialog.setOnCancel(new Runnable() {
+					@Override
+					public void run() {
+						synchronized (SyncCommand.this) {
+							confirmDecision = Boolean.FALSE;
+							confirmPending = false;
+							confirmDialog = null;
+							SyncCommand.this.notifyAll();
+						}
+					}
+				});
+				confirmDialog.showDialogNonBlocking();
+				while (confirmDecision == null) {
+					try {
+						this.wait();
+					} catch (InterruptedException e) {
+						Thread.currentThread().interrupt();
+						confirmPending = false;
+						if (confirmDialog != null) {
+							confirmDialog.closeDialog();
+							confirmDialog = null;
+						}
+						return false;
+					}
+				}
+				return confirmDecision.booleanValue();
+			}
+		}
 		GenericJTabbedDialog gd = new GenericJTabbedDialog("Stop requested, "+(convenient?"convenient point":"ASAP point"),600,300);
 		gd.addMessage ("OK to stop, Cancel to continue");
 		stopRequested.set(STOP_NO); // reset pending stop in any case.